It won't wipe anything. Even planted items will still be where they were before, which can look quite strange. I'd recommend taking everything out of the greenhouse first, but it's not required.
the problem i have with every single custom greenhouse is the warp location not being compatible with the custom immersive farm mod used with stardew valley expanded.
Yes, unfortunately SVE manually moves the warp point, making it have incompatibility issues with other mods. There's nothing I can do to change that at the moment :(
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